2-44320435-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_000341.4(SLC3A1):c.1854G>C(p.Met618Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000044 in 1,613,778 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Benign in Lovd.
Frequency
Consequence
NM_000341.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC3A1 | NM_000341.4 | c.1854G>C | p.Met618Ile | missense_variant | Exon 10 of 10 | ENST00000260649.11 | NP_000332.2 | |
PREPL | NM_001171613.2 | c.*921C>G | 3_prime_UTR_variant | Exon 14 of 14 | ENST00000409411.6 | NP_001165084.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC3A1 | ENST00000260649.11 | c.1854G>C | p.Met618Ile | missense_variant | Exon 10 of 10 | 1 | NM_000341.4 | ENSP00000260649.6 | ||
PREPL | ENST00000409411 | c.*921C>G | 3_prime_UTR_variant | Exon 14 of 14 | 1 | NM_001171613.2 | ENSP00000387095.2 | |||
ENSG00000285542 | ENST00000649044.1 | n.*1865G>C | downstream_gene_variant | ENSP00000497083.1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152026Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000401 AC: 10AN: 249352Hom.: 0 AF XY: 0.0000445 AC XY: 6AN XY: 134918
GnomAD4 exome AF: 0.0000472 AC: 69AN: 1461752Hom.: 0 Cov.: 50 AF XY: 0.0000468 AC XY: 34AN XY: 727196
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152026Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74232
ClinVar
Submissions by phenotype
Cystinuria Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at